Parametrization and penalties in spline models with an application to survival analysis

In this paper we show how a simple parametrization, built from the definition of cubic splines, can aid in the implementation and interpretation of penalized spline models, whatever configuration of knots we choose to use. We call this parametrization value-first derivative parametrization. We perform Bayesian inference by exploring the natural link between quadratic penalties and Gaussian priors. However, a full Bayesian analysis seems feasible only for some penalty functionals. Alternatives include empirical Bayes methods involving model selection type criteria. The proposed methodology is illustrated by an application to survival analysis where the usual Cox model is extended to allow for time-varying regression coefficients

Penalized spline models and applications

Penalized spline regression models are a popular statistical tool for curve fitting problems due to their flexibility and computational efficiency. In particular, penalized cubic spline functions have received a great deal of attention. Cubic splines have good numerical properties and have proven extremely useful in a variety of applications. Typically, splines are represented as linear combinations of basis functions. However, such representations can lack numerical stability or be difficult to manipulate analytically. The current thesis proposes a different parametrization for cubic spline functions that is intuitive and simple to implement. Moreover, integral based penalty functionals have simple interpretable expressions in terms of the components of the parametrization. Also, the curvature of the function is not constrained to be continuous everywhere on its domain, which adds flexibility to the fitting process. We consider not only models where smoothness is imposed by means of a single penalty functional, but also a generalization where a combination of different measures of roughness is built in order to specify the adequate limit of shrinkage for the problem at hand. The proposed methodology is illustrated in two distinct regression settings

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance. Background The mechanism for ambient temperature sensing in plants is unclear. Control of transcript levels is believed to be important in responses to temperature [1-4] but affects of ambient temperature on transcription and mRNA decay rates have not been measured. According to the work of Arrhenius [5] the temperature coefficient (Q10) of biochemical reactions is expected to be 2 to 3 at biological temperatures: yet less than 2% of Arabidopsis thaliana genes have a two-fold or greater difference in expression level between 17°C and 27°C [6]. The remaining genes either have rates buffered against changing temperatures, or passive increases in transcription rate must be offset by a balanced increase in decay rate, leading to higher turnover but static steady state levels. Despite this fundamental uncertainty, steady state transcriptomic responses to ambient temperature have been used to infer a role for chromatin modifications in temperature signaling [2,7]. 4-Thiouracil (4SU) is a non-toxic base analogue that has been shown to be incorporated into mammalian and yeast mRNA during transcription [8-12]. Biotinylation and column separation allow 4SU-labeled RNA to be separated from unlabeled RNA, and transcriptomic analysis using the separated samples can be used to simultaneously calculate mRNA synthesis and decay rates [8]. Here we use 4SU labeling to measure transcription rates and determine the Q10 genome-wide of mRNA synthesis and decay rates in Arabidopsis thaliana. We show that ambient temperature has large passive effects on both mRNA synthesis and decay rates, and that where temperature controls transcript abundance it does so by regulating transcription relative to decay and not vice versa. Our analysis suggests that transcription factor binding sites and epigenetic state combine to create a complex network of temperature responses in plants. Results Cells incorporate 4SU into RNA and this has been exploited in mammalian cells [8,11,12] and in yeast [13] to measure mRNA synthesis and decay rates. In order to determine whether plants can take up 4SU we floated intact seedlings in MS medium and monitored 4SU incorporation into RNA by biotinylation and dot blot (Figure S1a in Additional file 1). This clearly showed that plants incorporate 4SU from the environment into RNA and that concentrations as low as 1 mM lead to a signal detectable above background within 1 hour (Figure 1B). The resulting RNA could be separated from unlabeled RNA by biotinylation and passage through a streptavidin column as described previously. At 1.5 mM the flow-through can be depleted of detectable 4SU-labeled RNA, whilst labeled plant RNA is highly concentrated in the fraction recovered from the column [8,13] (Figure S1c in Additional file 1). To maximize recovery we chose a low concentration of 4SU at 1.5 mM [8] as high labeling frequencies are known to lead to binding of fewer more frequently labeled transcripts to the columns and reduce recovery. At this concentration Arabidopsis plants treated with 4SU showed the same growth and survival as control plants (Figure S2a in Additional file 1), suggesting 4SU has low toxicity in plants, as in other organisms. Therefore, 4SU dynamics in Arabidopsis seedlings resemble those described for other experimental systems. Preliminary experiments showed that RNA turnover was faster at 27°C compared to 12°C (Figure S2b in Additional file 1), suggesting that temperature generally affected transcription rates

A certificação de qualidade em sistemas solares para aquecimento de água

Tendo em atenção a política nacional para o desenvolvimento do mercado da Energia Solar Térmica, motivada pela necessidade de uma maior utilização das Energias Endógenas (Resolução do Conselho de Ministros nº154/2001 de 27 de Setembro), descreve-se a situação actual na área dos Equipamentos Solares para Aquecimento de Água, no que diz respeito à Certificação de Produtos e à Certificação de Pessoas, como medidas necessárias para a Garantia de Qualidade nesta área

On the sustainable development of solar thermal obligations in buildings in the framework of the Portuguese case

This paper starts remembering the steps given in Portugal to prepare the introduction of a solar thermal obligation. Next, it presents a description of the present legislation related to the Solar Thermal Obligation (STO) and to other incentive measures for growth of the solar thermal market in Portugal. The main problems with implementation of the new regulation are analysed and systematized. Based on the acquired knowledge, further actions are presented to guarantee the success of Solar Thermal Obligation, namely proposals for updating the obligation in conformity with best practice for solar thermal installations and taking into account the new realities upcoming from the actual solar therma

The LSTS open-source communication and autonomy software: enabling networked vehicle systems to find track, and sample dynamic features of the ocean

Peer Reviewe

Geographic variation in phenology behavior and response to drought of cork oak populations is crucial to cope with climate change

Cork oak is widely distributed in the Western Mediterranean region, spanning a range of different environmental conditions, and frequently dominating open woodlands of high conservation and socioeconomic value. Cork oak woodlands spread-out for over 715000 ha in Portugal, covering 21% of the national forested area and 30% of the world’s cork producing area. Cork oak is well adapted to the seasonal drought of Mediterranean climate, following several decades of warming- up and frequent drought years. However, since the 70's, maximum and minimum temperatures have risen in Portugal about 0.5 ºC each decade, corresponding to twice the average world temperature increment. In addition, since longer, more frequent, and more intense drought periods are expected, stress caused by the expansion of arid and semi-arid climate throughout the country will affect the species distribution. Consequently, not only established stands may be prone to tree mortality, but also the current reforestation effort may be jeopardized by low survival rates attributed to the use of unsuitable genetic material. It is expected that, through genetic adaptation and/or phenotypic plasticity, cork oak populations may have developed significant differences in fitness and the traits related to it. In this context, provenance trials are the best resource of material to assess the variability between and within populations from seed sources sampled in a wide range of locations (stands) covering the geographical distribution of the species. This will enable to assess the levels and patterns of genetic variation for growth and traits determining adaptation to a specific environment, hence providing crucial information to select appropriate seed sources for planting, as well as to develop sustainable breeding and gene conservation programs. In 1998, multi-site provenance trials were established at three locations in Portugal, as a part of the “European Network for the Evaluation of Genetic Resources of Cork Oak for Appropriate Use in Breeding and Gene Conservation Strategies”. Results from these field trials at 7 years from planting pointed out that seed origin must be considered in reforestation programs, since survival, growth and adaptive traits (phenology, water use efficiency - wue) showed significant differences among populations. Responses to drought (a major limitation to cork oak regeneration) of four contrasting populations, selected according to their field performance for growth, phenology and wue, were further studied under controlled-environment conditions where drought stress was induced. In addition, morphological (total height, root/shoot biomass), physiological (wue, water potential, relative water content and gas exchange) and biochemical (maximum quantum yield of PSII) traits were assessed in 6-month seedlings produced from acorns collected in the stands representing the four contrasting provenances. Results from the controlled experiment provided an indication that drought adaptation was mainly related to early stomatal closure and root investment, with these traits showing significant differences between the studied populations. We have also observed significant differences in growth rhythm, as well as dissimilar temporal drought responses, in the populations under study. In conclusion, both field trials and controlled environment showed consistent results and indicated an important influence of geographic origin on growth performance and wue.projeto PTDC/AGR-AAM/104364/200

Portuguese local government relative efficiency: a dea approach

It is widely accepted that performance measurement in the Public Sector is a difficult task, either in terms of efficiency or in terms of effectiveness. The most important reason for this relates to the lack of objective measures, given the market-aside operation of governmental activities. Therefore traditional methods of performance measurement, such as those based on the operating statement and the net income, tend fail. It is typical that public bodies’ outputs are multiple and qualitative and consequently do not have the physical characteristic of being countable or divisible. Portuguese Local Government has, in the last decade, undergone considerable management changes under the flag of efficiency improvement, namely additional competencies, supplementary and more diverse financial resources and a new accounting system. In this context, this paper assesses the efficiency of Portuguese Continental municipalities, using year 2004 data and following a data envelopment analysis (DEA) methodology in order to provide a relative efficiency indicator. The analysis compares the ratio between resources as inputs (“undertaken commitments”) and the activities accomplished as outputs, considering the functional classification used in municipalities’ accounting and financial system. This research adds to the knowledge of local authorities’ performance the possibility of establishing a functioning ranking, nowadays increasingly important in what concerns financing issues. The preliminary results show that larger municipalities tend to be more efficient.Fundação para a Ciência e a Tecnologia (FCT

The (Re)Industrialised Waterfront as a “Fluid Territory”: The Case of Lisbon and the Tagus Estuary

If delta and estuary areas are observed under the perspective of a double system of dynamic infrastructures, the object of parallel “water/urbanisation” processes, the interface spaces become key nodes. In this perspective, port and waterfront areas can be described as spaces of mediation. The article argues that in the case of Lisbon and the Tagus, as possibly in several other port cities, these edge spaces can be described as “fluid territories.” The pre-eminent characteristic of “fluid territories” is that they are not permanent, neither in space nor time. These areas present accelerated transformations, less defined boundaries, and an increased spatial and management complexity. Moreover, “fluid territories” also mediate (a) the culture-natural environment, with human action appropriating the natural system through infrastructure and urbanisation, and (b) the industrialised economic estuary, with its continuous updating. To demonstrate this hypothesis, two samples of Lisbon’s riverfront are observed, recording its constant variability over the last 200 years of industrialisation, emphasising the “fluidity” of the mediating spaces. The understanding of the “fluid” characteristic of water/land mediation spaces is relevant for the present. Being dynamic and regularly reinventing spaces, spatial planning, public space, and architectural design processes in “fluid territories” should increasingly seek adaptability, flexibility, and openness to change. In the climatic context of continuous uncertainty combined with the need to make room for infrastructure, rethinking mediation areas through the lens of the theoretical concept of the “fluid territory” enables the implementation of urban transformation processes consistent with contemporary challenges

Use of biogenic sulfide for the synthesis of CuS nanocrystals and nanocomposites

During the metabolism of organic matter (CH2O), sulfate-reducing bacteria (SRB) use sulfate as the terminal electron acceptor, resulting in the production of H2S. This biologically generated sulfide, in the presence of metal ions, can be used for metal precipitation (Bhagat et al., 2004). The use of SRB in bioremediation processes, namely, in the reduction of highcontent sulfate and metal effluents, is well documented (Costa and Duarte, 2005; Garcia et al., 2001). Nevertheless, the process generates an excess of sulfide and the elimination of the sulfide in excess and disposal of the metal sulfides produced are also problems that need to be carefully addressed. Copper monosulfide (CuS) has gained considerable attention in material science due to its excellent potential in catalysis (Mallick et al., 2007), optical functionality (Liz-Marzan, 2006) and electronic functionalities (Kamat, 2002)